Post-translational modification of proteins is a common and critical biochemical mechanism for altering the chemical nature of proteins, thus modulating their function. Examples of the biological effects of protein modifications include phosphorylation for signal transduction, ubiquitination for proteolysis, glycosylation for protein half-life, targeting, virahhost, cell:cell and celhmatrix interactions. Consequently, the analysis of proteins and their post-translational modifications is particularly important for the study of disease. The role of post-translational modifications (PTMs) of proteins in disease has been shown (refs). The best way to identify proteins and their PTMs in a high-throughput manner is by mass spectrometry (MS) Mann M, Jensen ON, Proteomic analysis of post-translational modifications NATURE BIOTECHNOLOGY 21 (3): 255-261 MAR 2003. Laugesen S, Bergoin A, Rossignol M Deciphering the plant phosphoproteorne: tools and strategies for a challenging task PLANT PHYSIOLOGY AND BIOCHEMISTRY 42 (12): 929-936 DEC 2004. Similarly the best method for characterizing metabolites in a high throughput, highly sensivitive manner is by MS (Kell, D. (2004) Metabolomics and systems biology: making sense of the soup. Curr Opin Microbiol 7,296-307). Fernie, A., R. Trethewey, A. Krotzky, and L. Willmitzer. (2004) Metabolite profiling: from diagnostics to systems biology. Nat Rev MolCell Biol 5,763-9. The current state-of-the-art instrument for identification and quantification of metabolites and PTMs is the Applied Biosystems 4000 Q TRAP. The 4000 Q TRAP is a hybrid MS that is a combination of a triple qudrupole and a linear ion trap that is ideal for high sensitivity identification of metabolites and proteins, PTMs, and quantification of the metabolite, protein, or PTMs. The 4000 Q TRAP is unique in that the typical triple quadruopole scanning events such as percursor ion and neutral loss can be automically linked to the high sensitivity ion trap tandem MS scans. The de-coupling of the precursor ion isolation and the fragmentation from the ion trap results in easily interpreted triple quadrupole fragmentation patterns with no inherent low mass cut off that is characteristic for ion trap instruments. When combined with the dual pump liquid chromatography system from LC-Packings, this LC-MS will allow researchers unique capabilities that are not currently available at Texas A&M University (TAMU). [unreadable] [unreadable]